Zinc in PDB 4hx3: Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Enzymatic activity of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
All present enzymatic activity of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin:
3.4.24.77;
Protein crystallography data
The structure of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin, PDB code: 4hx3
was solved by
S.Trillo-Muyo,
S.Martinez-Rodriguez,
J.L.Arolas,
F.X.Gomis-Ruth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.49 /
2.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.540,
121.810,
130.670,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
24.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
(pdb code 4hx3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin, PDB code: 4hx3:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 1 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:32.9
occ:1.00
|
OD1
|
A:ASP93
|
1.9
|
32.9
|
1.0
|
NE2
|
A:HIS87
|
2.1
|
35.4
|
1.0
|
NE2
|
A:HIS83
|
2.1
|
33.3
|
1.0
|
O
|
A:HOH323
|
2.2
|
28.7
|
1.0
|
CG
|
A:ASP93
|
2.8
|
34.2
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
35.2
|
1.0
|
CD2
|
A:HIS83
|
3.0
|
33.7
|
1.0
|
OD2
|
A:ASP93
|
3.1
|
44.9
|
1.0
|
CE1
|
A:HIS83
|
3.1
|
33.5
|
1.0
|
CD2
|
A:HIS87
|
3.2
|
35.9
|
1.0
|
OE2
|
A:GLU84
|
3.8
|
44.1
|
1.0
|
O
|
B:ALA32
|
3.9
|
39.9
|
1.0
|
O
|
B:HOH206
|
4.0
|
33.5
|
1.0
|
OE1
|
A:GLU84
|
4.1
|
43.4
|
1.0
|
ND1
|
A:HIS87
|
4.1
|
36.3
|
1.0
|
CG
|
A:HIS83
|
4.2
|
33.3
|
1.0
|
CB
|
A:ASP93
|
4.2
|
32.9
|
1.0
|
ND1
|
A:HIS83
|
4.2
|
34.7
|
1.0
|
CG
|
A:HIS87
|
4.2
|
34.2
|
1.0
|
CD
|
A:GLU84
|
4.3
|
46.1
|
1.0
|
NE2
|
B:HIS3
|
4.6
|
49.0
|
1.0
|
C
|
B:ALA32
|
4.7
|
38.0
|
1.0
|
OH
|
A:TYR95
|
4.8
|
35.5
|
1.0
|
CE1
|
B:HIS3
|
4.8
|
48.1
|
1.0
|
CA
|
B:TYR33
|
4.8
|
31.4
|
1.0
|
CE
|
A:MET103
|
4.8
|
29.7
|
1.0
|
CA
|
A:ASP93
|
4.9
|
31.3
|
1.0
|
|
Zinc binding site 2 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 2 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:43.8
occ:1.00
|
OD1
|
C:ASP93
|
1.9
|
50.0
|
1.0
|
O
|
C:HOH302
|
1.9
|
38.8
|
1.0
|
NE2
|
C:HIS83
|
2.1
|
35.9
|
1.0
|
NE2
|
C:HIS87
|
2.1
|
39.0
|
1.0
|
CG
|
C:ASP93
|
2.8
|
48.7
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
39.8
|
1.0
|
CD2
|
C:HIS83
|
3.0
|
35.8
|
1.0
|
OD2
|
C:ASP93
|
3.0
|
50.7
|
1.0
|
CE1
|
C:HIS83
|
3.1
|
36.7
|
1.0
|
CD2
|
C:HIS87
|
3.2
|
40.1
|
1.0
|
OE2
|
C:GLU84
|
3.7
|
53.3
|
1.0
|
O
|
D:ALA32
|
3.8
|
48.1
|
1.0
|
OE1
|
C:GLU84
|
4.2
|
52.3
|
1.0
|
ND1
|
C:HIS87
|
4.2
|
42.1
|
1.0
|
CG
|
C:HIS83
|
4.2
|
35.1
|
1.0
|
CB
|
C:ASP93
|
4.2
|
41.4
|
1.0
|
ND1
|
C:HIS83
|
4.2
|
37.3
|
1.0
|
CD
|
C:GLU84
|
4.2
|
53.6
|
1.0
|
CG
|
C:HIS87
|
4.2
|
40.7
|
1.0
|
C
|
D:ALA32
|
4.6
|
44.3
|
1.0
|
CA
|
D:TYR33
|
4.6
|
36.4
|
1.0
|
OH
|
C:TYR95
|
4.7
|
42.4
|
1.0
|
CE1
|
D:HIS3
|
4.7
|
71.9
|
1.0
|
NE2
|
D:HIS3
|
4.8
|
70.5
|
1.0
|
CE
|
C:MET103
|
4.8
|
41.1
|
1.0
|
CA
|
C:ASP93
|
4.9
|
42.1
|
1.0
|
|
Zinc binding site 3 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 3 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn201
b:50.7
occ:1.00
|
OD1
|
E:ASP93
|
1.9
|
54.1
|
1.0
|
NE2
|
E:HIS87
|
2.0
|
50.3
|
1.0
|
NE2
|
E:HIS83
|
2.1
|
49.8
|
1.0
|
O
|
E:HOH309
|
2.1
|
28.1
|
1.0
|
CG
|
E:ASP93
|
2.8
|
54.5
|
1.0
|
CE1
|
E:HIS87
|
2.9
|
50.8
|
1.0
|
CD2
|
E:HIS83
|
3.0
|
50.4
|
1.0
|
OD2
|
E:ASP93
|
3.1
|
59.1
|
1.0
|
CE1
|
E:HIS83
|
3.1
|
50.0
|
1.0
|
CD2
|
E:HIS87
|
3.1
|
51.6
|
1.0
|
OE2
|
E:GLU84
|
3.8
|
64.8
|
1.0
|
O
|
F:ALA32
|
3.9
|
46.9
|
1.0
|
O
|
F:HOH204
|
4.1
|
37.1
|
1.0
|
ND1
|
E:HIS87
|
4.1
|
53.0
|
1.0
|
CG
|
E:HIS83
|
4.2
|
49.5
|
1.0
|
CB
|
E:ASP93
|
4.2
|
46.8
|
1.0
|
CG
|
E:HIS87
|
4.2
|
51.4
|
1.0
|
OE1
|
E:GLU84
|
4.2
|
63.0
|
1.0
|
ND1
|
E:HIS83
|
4.2
|
51.4
|
1.0
|
CD
|
E:GLU84
|
4.3
|
72.5
|
1.0
|
C
|
F:ALA32
|
4.7
|
45.8
|
1.0
|
CA
|
F:TYR33
|
4.7
|
40.6
|
1.0
|
OH
|
E:TYR95
|
4.8
|
38.1
|
1.0
|
CE
|
E:MET103
|
4.8
|
48.4
|
1.0
|
NE2
|
F:HIS3
|
4.8
|
85.1
|
1.0
|
CA
|
E:ASP93
|
4.8
|
46.9
|
1.0
|
CE1
|
F:HIS3
|
5.0
|
83.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 4 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn201
b:41.6
occ:1.00
|
OD1
|
G:ASP93
|
1.9
|
38.6
|
1.0
|
NE2
|
G:HIS83
|
2.0
|
34.1
|
1.0
|
NE2
|
G:HIS87
|
2.0
|
31.7
|
1.0
|
O
|
G:HOH311
|
2.2
|
25.1
|
1.0
|
CG
|
G:ASP93
|
2.8
|
43.5
|
1.0
|
CE1
|
G:HIS87
|
2.9
|
31.7
|
1.0
|
CD2
|
G:HIS83
|
3.0
|
34.8
|
1.0
|
CE1
|
G:HIS83
|
3.1
|
34.9
|
1.0
|
OD2
|
G:ASP93
|
3.1
|
52.1
|
1.0
|
CD2
|
G:HIS87
|
3.1
|
32.4
|
1.0
|
O
|
H:ALA32
|
3.8
|
38.3
|
1.0
|
OE2
|
G:GLU84
|
3.8
|
42.8
|
1.0
|
O
|
H:HOH204
|
4.0
|
44.7
|
1.0
|
CG
|
G:HIS83
|
4.1
|
34.7
|
1.0
|
ND1
|
G:HIS87
|
4.1
|
32.8
|
1.0
|
CB
|
G:ASP93
|
4.2
|
41.5
|
1.0
|
ND1
|
G:HIS83
|
4.2
|
36.5
|
1.0
|
OE1
|
G:GLU84
|
4.2
|
55.8
|
1.0
|
CG
|
G:HIS87
|
4.2
|
31.6
|
1.0
|
CD
|
G:GLU84
|
4.3
|
46.3
|
1.0
|
C
|
H:ALA32
|
4.6
|
36.5
|
1.0
|
CA
|
H:TYR33
|
4.7
|
33.5
|
1.0
|
NE2
|
H:HIS3
|
4.7
|
51.9
|
1.0
|
CE
|
G:MET103
|
4.7
|
30.7
|
1.0
|
OH
|
G:TYR95
|
4.8
|
32.0
|
1.0
|
CA
|
G:ASP93
|
4.8
|
40.1
|
1.0
|
CE1
|
H:HIS3
|
4.9
|
51.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 5 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:36.6
occ:1.00
|
OD1
|
I:ASP93
|
2.0
|
37.5
|
1.0
|
NE2
|
I:HIS87
|
2.1
|
33.9
|
1.0
|
NE2
|
I:HIS83
|
2.1
|
37.3
|
1.0
|
O
|
I:HOH312
|
2.4
|
36.9
|
1.0
|
CG
|
I:ASP93
|
2.9
|
37.6
|
1.0
|
CD2
|
I:HIS83
|
3.0
|
37.3
|
1.0
|
CE1
|
I:HIS87
|
3.0
|
34.2
|
1.0
|
OD2
|
I:ASP93
|
3.1
|
42.7
|
1.0
|
CD2
|
I:HIS87
|
3.2
|
34.8
|
1.0
|
CE1
|
I:HIS83
|
3.2
|
37.2
|
1.0
|
OE1
|
I:GLU84
|
3.8
|
50.1
|
1.0
|
O
|
J:ALA32
|
3.9
|
42.6
|
1.0
|
O
|
J:HOH602
|
3.9
|
35.1
|
1.0
|
OE2
|
I:GLU84
|
4.2
|
58.1
|
1.0
|
CG
|
I:HIS83
|
4.2
|
35.9
|
1.0
|
CD
|
I:GLU84
|
4.2
|
51.5
|
1.0
|
ND1
|
I:HIS87
|
4.2
|
36.0
|
1.0
|
CG
|
I:HIS87
|
4.3
|
34.8
|
1.0
|
CB
|
I:ASP93
|
4.3
|
33.5
|
1.0
|
ND1
|
I:HIS83
|
4.3
|
37.8
|
1.0
|
NE2
|
J:HIS3
|
4.5
|
51.9
|
1.0
|
C
|
J:ALA32
|
4.7
|
41.6
|
1.0
|
CA
|
J:TYR33
|
4.8
|
36.8
|
1.0
|
CE1
|
J:HIS3
|
4.8
|
50.8
|
1.0
|
OH
|
I:TYR95
|
4.8
|
34.5
|
1.0
|
CE
|
I:MET103
|
4.9
|
32.3
|
1.0
|
|
Zinc binding site 6 out
of 6 in 4hx3
Go back to
Zinc Binding Sites List in 4hx3
Zinc binding site 6 out
of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn201
b:58.6
occ:1.00
|
OD1
|
K:ASP93
|
1.9
|
59.1
|
1.0
|
O
|
K:HOH301
|
1.9
|
36.7
|
1.0
|
NE2
|
K:HIS87
|
1.9
|
56.6
|
1.0
|
NE2
|
K:HIS83
|
2.0
|
62.9
|
1.0
|
CG
|
K:ASP93
|
2.8
|
59.6
|
1.0
|
CE1
|
K:HIS87
|
2.8
|
57.9
|
1.0
|
CD2
|
K:HIS83
|
3.0
|
63.6
|
1.0
|
CD2
|
K:HIS87
|
3.0
|
58.4
|
1.0
|
OD2
|
K:ASP93
|
3.1
|
65.3
|
1.0
|
CE1
|
K:HIS83
|
3.1
|
64.0
|
1.0
|
OE1
|
K:GLU84
|
3.9
|
58.7
|
1.0
|
O
|
L:ALA32
|
3.9
|
51.7
|
1.0
|
ND1
|
K:HIS87
|
4.0
|
61.5
|
1.0
|
CG
|
K:HIS87
|
4.1
|
60.1
|
1.0
|
CG
|
K:HIS83
|
4.1
|
63.0
|
1.0
|
CB
|
K:ASP93
|
4.2
|
56.8
|
1.0
|
OE2
|
K:GLU84
|
4.2
|
72.6
|
1.0
|
ND1
|
K:HIS83
|
4.2
|
65.3
|
1.0
|
CD
|
K:GLU84
|
4.3
|
75.5
|
1.0
|
CE1
|
L:HIS3
|
4.7
|
59.3
|
1.0
|
CE
|
K:MET103
|
4.7
|
69.0
|
1.0
|
C
|
L:ALA32
|
4.7
|
50.5
|
1.0
|
NE2
|
L:HIS3
|
4.7
|
57.6
|
1.0
|
CA
|
L:TYR33
|
4.8
|
47.6
|
1.0
|
OH
|
K:TYR95
|
4.8
|
51.2
|
1.0
|
CA
|
K:ASP93
|
4.8
|
58.0
|
1.0
|
|
Reference:
S.Trillo-Muyo,
S.Martinez-Rodriguez,
J.L.Arolas,
F.X.Gomis-Ruth.
Mechanism of Action of A Janus-Faced Single-Domain Protein Inhibitor Simultaneously Targeting Two Peptidase Classes Chem Sci V. 4 791 2013.
ISSN: ISSN 2041-6520
DOI: 10.1039/C2SC21712K
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